NIAS-Server 1.0 – Neighbors Influence of Amino acids and Secondary Structures in Proteins

NIAS-Server 1.0

:: DESCRIPTION

NIAS is a server to help the analysis of the conformational preferences of amino acid residues in proteins.

::DEVELOPER

SBCB – Structural Bioinformatics and Computational Biology Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

NIAS-Server: Neighbors Influence of Amino acids and Secondary Structures in Proteins.
Borguesan B, Inostroza-Ponta M, Dorn M.
J Comput Biol. 2016 Aug 5.

PSpro 2.0 – Predict Secondary Structure, Solvent Accessibility, and Residue-residue Contacts

PSpro 2.0

:: DESCRIPTION

PSpro is a software to predict secondary structure, solvent accessibility, and residue-residue contacts . It is essentially a bundle of three tools including SSpro 4.1, ACCpro 4.1 and NNcon 1.0.

::DEVELOPER

Dr. Jianlin Cheng’s Bioinformatics and Systems Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PSpro 

:: MORE INFORMATION

RME 1.1 – RNA Secondary Structure Prediction incorporating Experimental Constraints

RME 1.1

:: DESCRIPTION

RME predict RNA secondary structure by integrating the free energy model with probing data (SHAPE, PARS, DMS).

::DEVELOPER

Lu Lab, School of Life Sciences, Tsinghua University, China

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RME

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2015 Sep 3;43(15):7247-59. doi: 10.1093/nar/gkv706. Epub 2015 Jul 13.
Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data.
Wu Y, Shi B, Ding X, Liu T, Hu X, Yip KY, Yang ZR, Mathews DH, Lu ZJ

RNAex – RNA Secondary Structure Prediction Server

RNAex

:: DESCRIPTION

RNAex is an RNA secondary structure prediction enhanced by high-throughput experimental data

::DEVELOPER

Lu Lab, School of Life Sciences, Tsinghua University, China

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

RNAex: an RNA secondary structure prediction server enhanced by high-throughput structure-probing data.
Wu Y, Qu R, Huang Y, Shi B, Liu M, Li Y, Lu ZJ.
Nucleic Acids Res. 2016 May 2. pii: gkw362.

conSSert – Consensus Secondary Structure Prediction

conSSert

:: DESCRIPTION

conSSert is a SVM-based consenus secondary structure prediction method. Predictions from four popular secondary structure models (PSSpred, PSIPRED, Raptor-X, and SPINE-X) are integrated through the use of SVM models to produce highly accurate predictions, especially with regard to Q2-EH.

::DEVELOPER

the Multi-scale Systems Engineering Laboratory (MSEL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

conSSert: Consensus SVM model for accurate prediction of ordered secondary structure.
Kieslich CA, Smadbeck J, Khoury GA, Floudas C.
J Chem Inf Model. 2016 Feb 29.

SeqFold – Genome-scale Reconstruction of RNA Secondary Structure integrating Experimental Measurements

SeqFold

:: DESCRIPTION

SeqFold is a tool for RNA secondary structure prediction from experimental data. Given high-throughput data, it can reconstruct the secondary structures of the whole transcriptome, termed the RNA structurome.

::DEVELOPER

Ouyang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Python

:: DOWNLOAD

 SeqFold

:: MORE INFORMATION

Citation

Genome Res. 2013 Feb;23(2):377-87. doi: 10.1101/gr.138545.112. Epub 2012 Oct 11.
SeqFold: genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data.
Ouyang Z, Snyder MP, Chang HY.

RNABOB 2.2 – Fast Pattern Searching for RNA Secondary Structures

RNABOB 2.2

:: DESCRIPTION

RNABOB is an implementation of D. Gautheret’s RNAMOT, but with a different underlying algorithm using a nondeterministic finite state machine with node rewriting rules. (Computer scientists would probably cringe in horror. It works, and it’s fast, but is it street legal in a computer science department? Who knows.) An RNABOB motif is a consensus pattern a la PROSITE patterns, but with base-pairing.

::DEVELOPER

Sean Eddy, Eddy lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

  RNABOB

:: MORE INFORMATION

MetaSSPred – Balanced Secondary Structure Predictor

MetaSSPred

:: DESCRIPTION

MetaSSPred is a well-balanced Secondary Structure predictor

::DEVELOPER

Hoque’s Lab, University of New Orleans

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MetaSSPred

:: MORE INFORMATION

Citation

J Theor Biol. 2015 Nov 5;389:60-71. doi: 10.1016/j.jtbi.2015.10.015. [Epub ahead of print]
A balanced secondary structure predictor.
Nasrul Islam M, Iqbal S, Katebi AR, Tamjidul Hoque M

RNAentropy 1.0 – Compute RNA Secondary Structure Conformational Entropy

RNAentropy 1.0

:: DESCRIPTION

RNAentropy implements two cubic time algorithms to compute the RNA thermodynamic structural entropy.

::DEVELOPER

Clote Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RNAentropy

:: MORE INFORMATION

Citation

RNA Thermodynamic Structural Entropy.
Garcia-Martin JA, Clote P.
PLoS One. 2015 Nov 10;10(11):e0137859. doi: 10.1371/journal.pone.0137859.

RNAstructure 5.7 – Prediction & Analysis of RNA Secondary Structure

RNAstructure 5.7

:: DESCRIPTION

RNAstructure is a complete package for RNA and DNA secondary structure prediction and analysis. It includes algorithms for secondary structure prediction, including facility to predict base pairing probabilities. It also can be used to predict bimolecular structures and can predict the equilibrium binding affinity of an oligonucleotide to a structured RNA target. This is useful for siRNA design. It can also predict secondary structures common to two, unaligned sequences, which is much more accurate than single sequence secondary structure prediction. Finally, RNAstructure can take a number of different types of experiment mapping data to constrain or restrain structure prediction. These include chemical mapping, enzymatic mapping, NMR, and SHAPE data.

::DEVELOPER

Mathews Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac / Windows
  • Java

:: DOWNLOAD

RNAstructure

:: MORE INFORMATION

Citation

AccessFold: Predicting RNA-RNA Interactions with Consideration for Competing Self-Structure.
DiChiacchio L, Sloma MF, Mathews DH.
Bioinformatics. 2015 Nov 20. pii: btv682.

Reuter, J. S., & Mathews, D. H. (2010).
RNAstructure: software for RNA secondary structure prediction and analysis.
BMC Bioinformatics. 11,129.